Contacts of the strand formed by residues 145 - 153 (chain G) in PDB entry 1I3R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 145 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 4.0 16.2 - + - -
111G LYS 3.1 23.6 + - - -
112G PHE* 2.9 43.4 + - + +
113G SER* 4.0 6.3 - - - -
115G PRO* 3.7 37.2 - - + -
137G PHE* 3.8 20.6 - - + -
138G LEU 3.4 16.2 - - - +
140G ARG* 3.5 3.8 - - - +
143G HIS 4.0 9.4 - - - -
144G LEU* 1.3 75.5 - - - +
146G ARG* 1.3 63.9 + - - +
34H LEU* 3.9 13.2 - - + -
36H TYR* 3.4 48.9 - + - -
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Residues in contact with ARG 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ASP* 4.5 3.2 + - - -
28G GLY* 3.3 34.1 + - - -
108G PHE* 3.8 25.4 - - + -
109G ILE 3.1 9.0 - - - +
110G ASP* 3.4 15.0 - - - +
112G PHE* 3.8 2.2 - - - -
137G PHE* 3.8 1.9 - - - -
138G LEU* 2.8 68.0 + - + +
139G PRO 3.1 21.2 + - - -
140G ARG* 3.8 20.9 - - + +
145G PHE* 1.3 74.5 - - - +
147G LYS* 1.3 65.8 + - - +
148G PHE* 4.0 8.3 - - - -
175H ARG* 4.6 12.4 - - - +
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Residues in contact with LYS 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G CYS 3.6 1.4 - - - +
108G PHE* 3.7 4.2 - - - -
109G ILE* 2.7 41.5 + - + +
112G PHE* 4.2 11.9 - - + -
117G VAL* 4.2 12.7 + - + +
134G GLU* 3.0 20.2 + - - -
135G THR* 3.0 31.5 + - - +
136G VAL* 3.9 6.2 - - - +
137G PHE* 3.8 40.9 - - + -
138G LEU* 4.9 0.4 - - - -
146G ARG* 1.3 78.5 - - - +
148G PHE* 1.3 73.6 + - - +
149G HIS* 3.3 29.7 - - + +
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Residues in contact with PHE 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G ILE* 3.9 15.9 - - + -
107G CYS 3.6 2.2 - - - +
108G PHE* 3.4 40.6 - + + -
134G GLU* 3.3 4.6 - - - +
135G THR* 2.9 40.6 + - + +
138G LEU* 3.5 30.7 - - + -
146G ARG* 4.0 7.6 - - - -
147G LYS* 1.3 77.7 - - - +
149G HIS* 1.3 65.9 + - - +
150G TYR* 3.5 22.0 - - + +
175H ARG* 3.6 23.1 - - + -
176H ASN* 3.4 26.2 - - - -
177H GLY* 3.7 18.2 - - - -
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Residues in contact with HIS 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G ILE* 3.7 2.4 - - - +
107G CYS* 2.9 43.2 + - + +
109G ILE* 4.1 5.9 - - - +
117G VAL 5.9 0.2 - - - -
119G VAL* 3.4 50.4 + - + +
121G TRP* 3.5 19.4 - + - +
132G VAL* 6.2 1.3 - - + -
133G SER 3.4 7.4 - - - -
134G GLU* 3.1 28.7 + - + +
147G LYS* 3.3 34.3 - - + -
148G PHE* 1.3 76.1 + - - +
150G TYR* 1.3 65.6 + - - +
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Residues in contact with TYR 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ARG* 3.4 19.5 + - - -
94G ARG* 5.7 0.9 - - - -
104G ILE* 4.0 17.3 - - + -
105G LEU 3.4 2.2 - - - +
106G ILE* 3.9 29.6 - - + -
121G TRP* 3.3 8.4 + - - -
131G GLY 4.3 0.9 - - - -
132G VAL* 3.1 7.3 - - - -
133G SER* 2.7 58.4 + - - +
134G GLU* 4.6 1.8 - - - -
135G THR* 3.7 16.1 - - + +
148G PHE* 3.5 13.9 - - + +
149G HIS* 1.3 79.3 - - - +
151G LEU* 1.3 61.4 + - - +
176H ASN 2.6 29.4 + - - -
177H GLY* 3.2 21.8 + - - -
178H ASP* 4.8 9.6 - - + -
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Residues in contact with LEU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ILE* 3.3 4.8 - - - -
105G LEU* 2.7 39.8 + - + -
121G TRP* 3.6 39.9 - - + -
122G LEU 5.5 0.7 - - - +
123G ARG* 4.4 7.2 - - + +
128G VAL* 4.0 13.0 - - + -
130G GLU 4.0 9.4 - - - +
131G GLY 3.5 4.0 - - - +
132G VAL* 3.6 23.8 - - + -
150G TYR* 1.3 74.6 - - - +
152G THR* 1.3 76.6 + - - +
153G PHE* 3.5 2.6 + - + -
161G TYR* 3.7 36.3 - - + -
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Residues in contact with THR 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G ASN 3.6 8.5 - - - +
104G ILE* 4.5 16.6 - - + -
123G ARG* 3.3 16.1 + - - -
130G GLU 4.5 1.4 + - - +
131G GLY* 3.0 35.6 + - - +
151G LEU* 1.3 77.3 - - - +
153G PHE* 1.3 58.4 + - - +
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Residues in contact with PHE 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G SER* 5.0 0.9 - - - -
97G VAL* 4.6 5.6 - - + -
102G PRO* 3.9 1.8 - - - +
103G ASN* 3.0 58.4 + - + -
104G ILE 3.6 15.9 - - - -
105G LEU* 3.6 28.5 - - + -
123G ARG* 3.9 9.6 - - - +
151G LEU* 4.4 3.8 - - + +
152G THR* 1.3 75.2 - - - +
154G LEU* 1.3 61.6 + - - +
155G PRO* 3.4 33.5 - - + +
161G TYR* 3.6 36.3 - + + +
178G TRP* 3.9 31.2 - + - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il